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Capturing variation impact on molecular interactions: the IMEx Consortium mutations data set

The IMEx Consortium Curators, View ORCID ProfileN del Toro, View ORCID ProfileM Duesbury, View ORCID ProfileM Koch, View ORCID ProfileL Perfetto, View ORCID ProfileA Shrivastava, View ORCID ProfileD Ochoa, View ORCID ProfileO Wagih, View ORCID ProfileJ Piñero, M Kotlyar, C Pastrello, View ORCID ProfileP Beltrao, View ORCID ProfileLI Furlong, View ORCID ProfileI Jurisica, View ORCID ProfileH Hermjakob, View ORCID ProfileS Orchard, View ORCID ProfileP Porras
doi: https://doi.org/10.1101/346833
1European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
N del Toro
1European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
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M Duesbury
1European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
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M Koch
1European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
2Novartis Institutes for BioMedical Research (NIBR), Basel, Canton of Basel-Stadt, Switzerland
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L Perfetto
1European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
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A Shrivastava
1European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
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D Ochoa
1European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
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O Wagih
1European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
3Deep Genomics, MaRS Centre, 661 University Ave, Suite 480, Toronto, Ontario, M5G 1M1, Canada
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J Piñero
4Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences (DCEXS), Hospital del Mar Medical Research Institute (IMIM), Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
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M Kotlyar
5Krembil Research Institute, Data Science Discovery Centre for Chronic Diseases, Krembil Discovery Tower, 5KD-407, 60 Leonard Avenue, Toronto, Ontario, M5T 0S8, Canada
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C Pastrello
5Krembil Research Institute, Data Science Discovery Centre for Chronic Diseases, Krembil Discovery Tower, 5KD-407, 60 Leonard Avenue, Toronto, Ontario, M5T 0S8, Canada
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P Beltrao
1European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
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LI Furlong
4Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences (DCEXS), Hospital del Mar Medical Research Institute (IMIM), Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
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I Jurisica
5Krembil Research Institute, Data Science Discovery Centre for Chronic Diseases, Krembil Discovery Tower, 5KD-407, 60 Leonard Avenue, Toronto, Ontario, M5T 0S8, Canada
6Departments of Medical Biophysics and Computer Science, University of Toronto
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H Hermjakob
1European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
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S Orchard
1European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
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P Porras
1European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
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  • For correspondence: pporras@ebi.ac.uk
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Abstract

The current wealth of genomic variation data identified at the nucleotide level has provided us with the challenge of understanding by which mechanisms amino acid variation affects cellular processes. These effects may manifest as distinct phenotypic differences between individuals or result in the development of disease. Physical interactions between molecules are the linking steps underlying most, if not all, cellular processes. Understanding the effects that amino acid variation of a molecule’s sequence has on its molecular interactions is a key step towards connecting a full mechanistic characterization of nonsynonymous variation to cellular phenotype. Here we present an open access resource created by IMEx database curators over 14 years, featuring 28,000 annotations fully describing the effect of individual point sequence changes on physical protein interactions. We describe how this resource was built, the formats in which the data content is provided and offer a descriptive analysis of the data set. The data set is publicly available through the IntAct website at www.ebi.ac.uk/intact/resources/datasets#mutationDs and is being enhanced with every monthly release.

Contributions

S.O. and P.P. designed this study and wrote the manuscript. The IMEx Consortium curators generated the mutation annotations. M.D., S.O., M. Koch, N.dT., A.S. and P.P. re-curated the data set and implemented semi-automated quality control procedures. L.P., D.O., O.W., C.P., M. Kotlyar, J.P. and P.P. analysed the data. S.O., H.H., P.B., L.I.F., I.J. and P.P. interpreted the results and revised the manuscript.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted June 22, 2018.
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Capturing variation impact on molecular interactions: the IMEx Consortium mutations data set
The IMEx Consortium Curators, N del Toro, M Duesbury, M Koch, L Perfetto, A Shrivastava, D Ochoa, O Wagih, J Piñero, M Kotlyar, C Pastrello, P Beltrao, LI Furlong, I Jurisica, H Hermjakob, S Orchard, P Porras
bioRxiv 346833; doi: https://doi.org/10.1101/346833
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Capturing variation impact on molecular interactions: the IMEx Consortium mutations data set
The IMEx Consortium Curators, N del Toro, M Duesbury, M Koch, L Perfetto, A Shrivastava, D Ochoa, O Wagih, J Piñero, M Kotlyar, C Pastrello, P Beltrao, LI Furlong, I Jurisica, H Hermjakob, S Orchard, P Porras
bioRxiv 346833; doi: https://doi.org/10.1101/346833

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